Membrane’s digest

MP

Time-resolved cryo-EM of G-protein activation by a GPCR.

Papasergi-Scott MM, Pérez-Hernández G, Batebi H, Gao Y, Eskici G, Seven AB, Panova O, Hilger D, Casiraghi M, He F, Maul L, Gmeiner P, Kobilka BK, Hildebrand PW, Skiniotis G.

Nature. 2024 Mar 13.

doi: 10.1038/s41586-024-07153-1. PMID: 38480881.

Time-resolved cryo-EM approach to visualize the dynamic process of G-protein activation by GPCRs: examination of the sequential intermediates of a GPCR-G-protein complex => conformational trajectory underlying G-protein activation and dissociation from.

Structural analysis => structural changes initiated by GTP binding propagate through the G-protein, resulting in alterations to key regions that weaken the G-protein-receptor interface.

MD support the observed destabilization of the α5 helix => eventual dissociation of the G protein from the GPCR.

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The role of G protein-coupled receptor kinases in GLP-1R β-arrestin recruitment and internalisation.

McNeill SM, Lu J, Marion C Carino C, Inoue A, Zhao P, Sexton PM, Wootten D.

Biochem Pharmacol. 2024 Mar 8:116119.

doi: 10.1016/j.bcp.2024.116119. PMID: 38461904.

The glucagon-like peptide 1 receptor (GLP-1R) = validated clinical target for the treatment of type 2 diabetes and obesity.

GLP-1R = atypical mode of internalisation that does not require β-arrestins.

The role of G protein-coupled receptor kinases (GRKs) in affecting trafficking and recruitment has not been comprehensively assessed.

Here: quantification of the contribution of GRKs to agonist-mediated GLP-1R internalisation and β-arrestin recruitment profiles => atypical β-arrestin-independent mode of GLP-1R internalisation + GLP-1R internalisation dependent on the expression of GRKs.

The recruitment of GLP-1R is differentially affected by β-arrestin 1 or β-arrestin 2 => β-arrestin 1 recruitment more sensitive to GRK knockout than β-arrestin 2 recruitment.

Individual overexpression of GRK2, GRK3, GRK5 or GRK6 rescued agonist-mediated β-arrestin 1 recruitment and internalisation profiles to similar levels.

Arrestin-centred interactions at the membrane and their conformational determinants.

Underwood O, Haider RS, Sanchez J, Canals M.

Br J Pharmacol. 2024 Mar 13. doi: 10.1111/bph.16331. PMID: 38479842.

Review of the most recent advances on GPCR-arrestin complexes, from structure to interactions of arrestins with the lipid bilayer and other proteins + view on the development of tools to study the conformational flexibility of arrestins.

VMAT structures reveal exciting targets for drug development.

Schuldiner S, Forrest LR.

Trends Pharmacol Sci. 2024 Feb 29:S0165-6147(24)00031-2.

doi: 10.1016/j.tips.2024.02.004. PMID: 38429134.

Vesicular monoamine transporter (VMAT)-2 = crucial role in the neurotransmission of biogenic amines. Recent cryoEM structures of human VMAT2 = opportunities for  improved therapeutics and deep insights into the functioning of this protein.

TrkB transmembrane domain: bridging structural understanding with therapeutic strategy.

Enkavi G, Girych M, Moliner R, Vattulainen I, Castrén E.

Trends Biochem Sci. 2024 Mar 2:S0968-0004(24)00037-9.

doi: 10.1016/j.tibs.2024.02.001. PMID: 38433044.

TrkB (neuronal receptor tyrosine kinase-2, NTRK2) = receptor for brain-derived neurotrophic factor (BDNF). TrkB interacts with membrane cholesterol, which bidirectionally regulates signaling. Antidepressants act as allosteric potentiators of BDNF signaling through TrkB.

The TAM, a Translocation and Assembly Module for protein assembly and potential conduit for phospholipid transfer.

Goh KJ, Stubenrauch CJ, Lithgow T.

EMBO Rep. 2024 Mar 11.

doi: 10.1038/s44319-024-00111-y. PMID: 38467907.

Review on TAM (= module of the BAM machinery) is a heterodimeric complex composed of an OM protein (TamA) bound to IM protein (TamB).

The TAM spans the periplasm =>  scaffold through PG + catalysis of the translocation and assembly of β-barrel proteins into the OM.

Recently, studies on YhdP (MP) suggested that TamB might play a role in PL transport to OM.

The crossing of two unwound transmembrane regions that is the hallmark of the NhaA structural fold is critical for antiporter activity.

Rimon A, Amartely H, Padan E.

Sci Rep. 2024 Mar 11;14(1):5915.

doi: 10.1038/s41598-024-56425-3. PMID: 38467695.

NhaA = Na+/H+ antiporters => pH and Na+ homeostasis.

Xtal structure of E. coli NhaA => out of the 12 TMs, TMs III-V and X-XII are topologically inverted repeats with unwound TMs IV and XI forming the X shape characterizing the NhaA fold.

Here: intramolecular cys X-linking => inhibition of the antiporter activity + impairement of NhaA-dependent cell growth in high-salts. The cross-linking traps the antiporter in an OF conformation, blocking the antiport cycle.

De novo-designed transmembrane proteins bind and regulate a cytokine receptor.

Mravic M, He L, Kratochvil HT, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF.

Nat Chem Biol. 2024 Mar 13.

doi: 10.1038/s41589-024-01562-z. PMID: 38480980.

Computational design of de novo transmembrane proteins targeting the erythropoietin receptor (EpoR) TM domain, effectively competing with receptor homodimerization and inhibiting EPO-induced cell proliferation when expressed in mammalian cells. Synthetic TM domain complexes outcompete EpoR homodimerization in vitro, with structural characterization confirming the involvement of intended amino acids and supporting the designed molecular model of antiparallel TM helices at 1:1 stoichiometry.

Transmembrane β-Barrel Proteins Methods and Protocols

edited by Raffaele Ieva

Methods in Molecular Biology (MIMB, volume 2778)

https://link.springer.com/book/10.1007/978-1-0716-3734-0#about-this-book

Volume = experimental techniques and protocols for the expression, assembly, characterization, and utilization of transmembrane β-barrel proteins. => methodologies for studying assembly, characterizing interactions with cellular factors, dissecting protein transport processes in bacteria and mitochondria, and structural characterization and prediction.

Membranes

Phospholipid Membranes as Chemically and Functionally Tunable Materials.

Huster D, Maiti S, Herrmann A.

Adv Mater. 2024 Mar 8:e2312898.

doi: 10.1002/adma.202312898. PMID: 38456771.

Review on an emerging field = membrane-associated material properties of different bilayer systems used in designing innovative solutions for food industry, cosmetics, nano- and biomedicine, drug storage and delivery, biotechnology, nano- and biosensors, and computing.

Domain-Targeted Membrane Partitioning of Specific Proteins with DNA Nanodevices.

Ma YH, Zhu Y, Wu H, He Y, Zhang Q, Huang Q, Wang Z, Xing H, Qiu L, Tan W.

J Am Chem Soc. 2024 Mar 11.

doi: 10.1021/jacs.3c13966. PMID: 38466380.

The ability to manipulate the partitioning of specific membrane proteins without involving genetic modification = essential for decoding cellular processes.

Here: by conjugating cholesterols or tocopherols at the three bottom vertices of a DNA tetrahedron, authors develop two sets of nanodevices for the selective targeting of lipid-order (Lo) and lipid-disorder (Ld) domains on the live cell membrane.

Incorporation of protein-recognition ligands => the DNA nanodevices enable dynamic translocation of target proteins between these two domains.

A binding site for phosphoinositides described by multiscale simulations explains their modulation of voltage-gated sodium channels.

Lin Y, Tao E, Champion JP, Corry B.

Elife. 2024 Mar 11;12:RP91218.

doi: 10.7554/eLife.91218. PMID: 38465747.

Voltage-gated sodium channels (Naᵥ) = MPs which open to facilitate the inward flux of Na+ into excitable cells. In response to stimuli, Naᵥ channels transition from the resting, closed state to an open, conductive state, before rapidly inactivating.

Phosphoinositides = important lipid cofactors for ion channel function. PI(4,5)P2 decreases Naᵥ1.4 activity by lowering channel opening => fast inactivation and slowing recovery from fast inactivation.

MD => PI(4,5)P2 binds stably to inactivated Naᵥ at a conserved site which couples the voltage-sensing domain (VSD) to the pore.

In resting state, phosphoinositides bind to VSD gating charges => may impede VSD activation.

Molecular Crowding Alters the Interactions of Polymyxin Lipopeptides within the Periplasm of E. coli: Insights from Molecular Dynamics.

Smith IPS, Pedebos C, Khalid S.

J Phys Chem B. 2024 Mar 8.

doi: 10.1021/acs.jpcb.3c07985. PMID: 38457439.

Little is known about the mechanisms via which antimicrobial peptides move through the periplasm from OM to the IM (their site of action).

All-atom MD to study polymyxins B1 and E, within models of the E.coli periplasm crowded to different extents.

If in a simple chemical environment => PMB1 and PME bind irreversibly to the cell wall.

If presence of specific macromolecules => competition with the polymyxins for cell wall interaction sites => polymyxin dissociate from the cell wall.

Chemical complexity also impacts interactions between polymyxins and Braun’s lipoprotein.

Molecules

Surfmer versus Polymer Effect toward Solubilization and Stabilization of Membrane Proteins

Floriane Mangin, Vinay Chauhan, Pierre Guillet, Marjorie Damian, Marine Soulié, Jean-Louis Banères, and Grégory Durand

ACS Applied Polymer Materials Article ASAP

DOI: 10.1021/acsapm.3c02858

Synthesis of 4 acrylamide-based monomers (“surfmers”), featuring glucose or maltose headgroups and hydrophobic alkyl chains, which were polymerized to form nonionic polymers through free-radical telomerization.

Polymerization: high reproducibility and control =>narrow polydispersity and forming small homogeneous aggregates of 5 nm diameter (monomers) and 5 to 16 nm diameter (polymers), as indicated by surface tension and dynamic light scattering measurements.

Distinct roles of surfmers and polymers in solubilizing and stabilizing fragile membrane proteins: surfmers efficiently solubilized ghrelin receptor GHSR from membrane fractions, while polymers were more effective at stabilizing its functional fold in solution.

Novel class of peptides disintegrating biological membranes to aid in the characterization of membrane proteins.

Hořejší V, Angelisová P, Pokorná J, Charnavets T, Benada O, Čajka T, Brdička T.

J Biol Chem. 2024 Mar 11:107154.

doi: 10.1016/j.jbc.2024.107154. PMID: 38479603.

Investigation of the efficacy of amphiphilic peptides, structurally resembling SMA, in disintegrating cell membranes to produce lipid NP/ND containing MPs in a native-like lipid environment.

Unlike SMA these peptides offer structural homogeneity and effective membrane-disrupting properties, with activity peaking at 24 amino acids length and requiring a basic primary structure (XXD)n, where X is a hydrophobic amino acid, D is aspartic acid.

A DNA tetrahedron dimer for dual membrane protein logic recognition and interaction inhibition.

Zhang Y, Lin M, Yao J, Xu X.

Chem Commun (Camb). 2024 Mar 14.

doi: 10.1039/d4cc00479e. PMID: 38482771.

Report of a DNA tetrahedron dimer for dual membrane protein logic recognition and interaction inhibition. The DNA tetrahedron dimer not only detects dual proteins that are both overexpressed on target cells in “AND” logic, but also inhibits protein interaction by steric hindrance to suppress cell proliferation, offering new insights for cancer cell diagnosis and treatment.

Miscellaneous

Good reasons for structural biology.

Cramer P.

Nat Struct Mol Biol. 2024 Mar 1.

doi: 10.1038/s41594-024-01232-7. PMID: 38429440.

Safety guidelines for AI-designed proteins

https://www.nature.com/articles/d41586-024-00699-0?utm_source=Live+Audience&utm_campaign=35b1b6f44e-briefing-dy-20240311&utm_medium=email&utm_term=0_b27a691814-35b1b6f44e-50537092

Researchers have launched an initiative calling for the safe and ethical use of protein design. The voluntary effort comes on the heels of reports from lawmakers, think tanks and other organizations exploring the possibility that AI tools — ranging from protein-structure prediction networks such as AlphaFold to large language models such as the one that powers ChatGPT — could make it easier to develop biological weapons, including new toxins or highly transmissible viruses. The new initiative calls for the biodesign community to police itself and for improved screening of DNA synthesis, a key step in making AI-designed proteins, for potentially harmful molecules.

The wwPDB Consortium , EMDB—the Electron Microscopy Data Bank.

Nucleic Acids Research, Volume 52, Issue D1, 5 January 2024, Pages D456–D465.

https://doi.org/10.1093/nar/gkad1019

from the CCP4BB: ”The burgeoning popularity of the electron EM has been coupled with new technologies and software solutions, together this has pushed exponential growth in yearly depositions, increases in the resolution of the deposited data, and, consequently, accuracy of molecule models associated with 3DEM data. As the EMDB continues to grow it remains dedicated to delivering a world-class archive that adheres to FAIR principles. In addition, we recognise the importance of easy and open access to accurately curated data for the various users of the archive, we plan to continue to facilitate and enhance this moving forward”.

Why sunsets were a weird colour after Krakatau blew its top

Nature 627, 247 (2024)

doi: https://doi-org.insb.bib.cnrs.fr/10.1038/d41586-024-00601-y

Following the 1883 eruption of the Krakatau volcano in Indonesia, instead of the typical red skies, green-colored sunsets were observed worldwide, attributed to the size and distribution of volcanic particles ejected during the event. While large volcanic eruptions often lead to red sunsets due to increased atmospheric particle scattering, the unique green skies following the Krakatau eruption prompted researchers led by Christian von Savigny at the University of Greifswald to model atmospheric conditions, suggesting that particles of 500–700 nanometers in radius were responsible for the phenomenon. Analyzing historical records of volcanic skies aids in understanding the magnitude of past eruptions and their atmospheric effects.

Will these reprogrammed elephant cells ever make a mammoth?

Nature 627, 253-254 (2024)

doi: https://doi-org.insb.bib.cnrs.fr/10.1038/d41586-024-00670-z

Colossal Biosciences achieved a breakthrough by converting elephant cells into an embryonic state, a crucial step in their project to engineer elephants with woolly mammoth traits. Despite challenges in establishing elephant induced pluripotent stem (iPS) cells, the successful creation of four iPS-cell lines from an elephant opens avenues for genetic editing and studying mammoth traits in Asian elephants. While the technology is promising, further advancements are necessary for the ambitious goal of creating mammoth-like elephants, potentially requiring artificial wombs and additional reproductive biology leaps.